Thank you to everyone who submitted bug reports and patiently waited for me to respond.

Remember that now tutorials and the core code are kept separate. The core circos-0.56.tgz archive contains an example directory (example/) that creates a relatively complex image. Use this to ensure that everything is working.

Most of the changes are bug fixes. Error handling is improved - many errors have a gentler format and should be more explanatory.

*** IMPORTANT CHANGES AND REMINDERS ***

1. Import colors/fonts/patterns all at once

Use a single line to add color, font and pattern definitions in circos.conf:

<<include etc/colors_fonts_patterns.conf>>

instead of

<colors> <<include etc/colors.conf>> ...

Note that colors.conf now imports brewer.conf automatically.

Please see example/etc/circos.conf for ideas of how to make your configuration more modular.

2. Make sure you're using etc/housekeeping.conf

A while back, I had centralized system parameters that used to appear at the bottom of circos.conf into a separate file. For those of you who still have these parameters in their circos.conf file, please remove them.

I've revamped how SVG text labels are placed. You'll notice that fonts now have font family definitions in etc/fonts.conf. This string is used in the SVG file to specify the font. Once you have the font installed on your system, labels won't all appear in the SVG app or viewer default (e.g. Arial) font.

There's still more to do here, but it's getting better.

0.56 CHANGELOG

Parallel ideogram labels are now centered with respect to the ideogram.

restrict_parameter_names now controls whether parameters are restricted to a pre-defined list (e.g. color, thickness, etc). If you have custom parameters (e.g. 'myspecialcode') then set restrict_parameter_names=no. By default, this is always set to 'yes'.

Added link_orientation for text tracks. When set to "out" links from text labels face out, rather than in.

Added font names to SVG files via font-family tag.

Removed -verbose. The -v flag now reports version.

Removed dependence on Graphics::ColorObject.

Added error handling framework.

Circos now requires Text::Format

Bug fix to heat map color mapping of last color.

Fixed bug which was causing line links to be drawn with a thickness half of what was requested.

Fixed bug that prevented parameters made acceptable by the restrict_parameter_names=no setting from being parsed.

Configuration file location is now guessed if guess_conf_location=yes (see etc/housekeeping.conf)

Color file cache can now be static (color_cache_static) and dir/file can be changed (color_cache_{file,dir})

Added 'placed' and 'not_placed' output for labels in text tracks to. Use -debug_group text to see this.